I have successfully run the commands and finished the analysis using leafcutter. But deferentially spliced intron for p.value(FDR),0.05 are more than 10000 deferentially spliced introns but other publication got only 80-100 deferentially spliced introns. I wanted to know where I have gone wrong. Below are the list of commands I have used. It would be great if you anyone can help me on this
Step1)
for bamfile in `ls /data/STAR_BAM/*.bam`
do
echo Converting $bamfile to $bamfile.junc
sh /home/softwares/leafcutter/leafcutter/scripts/bam2junc.sh $bamfile $bamfile.junc
echo $bamfile.junc >> test_juncfiles.txt
done
Step2)
python ../clustering/leafcutter_cluster.py -j test_juncfiles.txt -m 50 -o testYRIvsEU -l 500000
Step3)
/leafcutter/scripts/leafcutter_ds.R --num_threads 16 --exon_file=/data/leafcutter/scripts/gencode.v29.exons.txt.gz ./testYRIvsEU_perind_numers.counts.gz ./groups_file.txt
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